Ecological security is one of the foundations of national security, and is the basis of regional sustainable development. Regional ecological security includes ecological-environmental security, economic security and social security. On the basis of the development of the eco-economic system of Zhifanggou Valley in the Loess Hilly Region over 70 years, based on historical research and related literature, and with the Pressure-State-Response (PSR) model framework as a foundation, a 3-layer conceptual assessment index system for the agricultural eco-security, which included ecological-environment, socio-economic, and integrated functions, was established for the Loess Hilly Region. Using the Analytic Hierarchy Process (AHP) and an integrating index evaluation method, the Zhifanggou Valley was used as a case study and its agricultural eco-security status, from 1938 to 2005, was assessed quantitatively. The results showed that its Ecological Security Integrated Value (ESIV) had a trend of unsafe to safe. The valley was in a relatively safe and a very unsafe state in 1938 and 1958, respectively; in an unsafe condition in 1975 and 1985; and in a critically safe and a relatively safe state in 1995 and 2005, respectively. The research results indicated that the agricultural system structure of the Zhifanggou Valley is still in need of further optimization for realizing agricultural eco-security.